Starting phenix.real_space_refine on Thu Mar 5 13:44:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7uzm_26915/03_2026/7uzm_26915.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uzm_26915/03_2026/7uzm_26915.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7uzm_26915/03_2026/7uzm_26915.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uzm_26915/03_2026/7uzm_26915.map" model { file = "/net/cci-nas-00/data/ceres_data/7uzm_26915/03_2026/7uzm_26915.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uzm_26915/03_2026/7uzm_26915.cif" } resolution = 3.24 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.039 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 108 5.16 5 C 14352 2.51 5 N 3996 2.21 5 O 4296 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22752 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 3793 Classifications: {'peptide': 494} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 22, 'TRANS': 471} Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 2, 'HIS:plan': 1, 'TYR:plan': 1, 'GLN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "B" Number of atoms: 3793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 3793 Classifications: {'peptide': 494} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 22, 'TRANS': 471} Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 2, 'HIS:plan': 1, 'TYR:plan': 1, 'GLN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "C" Number of atoms: 3793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 3793 Classifications: {'peptide': 494} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 22, 'TRANS': 471} Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 2, 'HIS:plan': 1, 'TYR:plan': 1, 'GLN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "D" Number of atoms: 3793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 3793 Classifications: {'peptide': 494} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 22, 'TRANS': 471} Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 2, 'HIS:plan': 1, 'TYR:plan': 1, 'GLN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "E" Number of atoms: 3793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 3793 Classifications: {'peptide': 494} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 22, 'TRANS': 471} Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 2, 'HIS:plan': 1, 'TYR:plan': 1, 'GLN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "F" Number of atoms: 3787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 3787 Classifications: {'peptide': 494} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 22, 'TRANS': 471} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 2, 'HIS:plan': 1, 'TYR:plan': 1, 'GLN:plan1': 1, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 41 Time building chain proxies: 5.51, per 1000 atoms: 0.24 Number of scatterers: 22752 At special positions: 0 Unit cell: (119.88, 112.32, 167.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 108 16.00 O 4296 8.00 N 3996 7.00 C 14352 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.88 Conformation dependent library (CDL) restraints added in 1.2 seconds 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5364 Finding SS restraints... Secondary structure from input PDB file: 126 helices and 9 sheets defined 59.5% alpha, 10.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'A' and resid 65 through 89 removed outlier: 3.631A pdb=" N VAL A 86 " --> pdb=" O GLU A 82 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N GLU A 87 " --> pdb=" O ASP A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 94 removed outlier: 3.611A pdb=" N SER A 94 " --> pdb=" O ARG A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 110 Processing helix chain 'A' and resid 157 through 175 removed outlier: 3.659A pdb=" N VAL A 175 " --> pdb=" O LYS A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 212 Processing helix chain 'A' and resid 229 through 244 removed outlier: 3.735A pdb=" N MET A 233 " --> pdb=" O GLY A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 254 Processing helix chain 'A' and resid 259 through 263 Processing helix chain 'A' and resid 267 through 285 removed outlier: 4.414A pdb=" N THR A 272 " --> pdb=" O ARG A 268 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N GLY A 273 " --> pdb=" O ILE A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 294 removed outlier: 3.560A pdb=" N MET A 290 " --> pdb=" O GLU A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 324 Processing helix chain 'A' and resid 344 through 356 Processing helix chain 'A' and resid 370 through 374 Processing helix chain 'A' and resid 391 through 396 removed outlier: 3.910A pdb=" N ARG A 395 " --> pdb=" O SER A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 421 Processing helix chain 'A' and resid 426 through 431 Processing helix chain 'A' and resid 432 through 448 Processing helix chain 'A' and resid 455 through 478 Processing helix chain 'A' and resid 490 through 499 Processing helix chain 'A' and resid 501 through 528 removed outlier: 3.772A pdb=" N ILE A 505 " --> pdb=" O SER A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 553 Processing helix chain 'B' and resid 65 through 89 removed outlier: 3.631A pdb=" N VAL B 86 " --> pdb=" O GLU B 82 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N GLU B 87 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 94 removed outlier: 3.612A pdb=" N SER B 94 " --> pdb=" O ARG B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 110 Processing helix chain 'B' and resid 157 through 175 removed outlier: 3.658A pdb=" N VAL B 175 " --> pdb=" O LYS B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 212 Processing helix chain 'B' and resid 229 through 244 removed outlier: 3.735A pdb=" N MET B 233 " --> pdb=" O GLY B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 254 Processing helix chain 'B' and resid 259 through 263 Processing helix chain 'B' and resid 267 through 285 removed outlier: 4.413A pdb=" N THR B 272 " --> pdb=" O ARG B 268 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N GLY B 273 " --> pdb=" O ILE B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 294 removed outlier: 3.560A pdb=" N MET B 290 " --> pdb=" O GLU B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 324 Processing helix chain 'B' and resid 344 through 356 Processing helix chain 'B' and resid 370 through 374 Processing helix chain 'B' and resid 391 through 396 removed outlier: 3.910A pdb=" N ARG B 395 " --> pdb=" O SER B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 421 Processing helix chain 'B' and resid 426 through 431 Processing helix chain 'B' and resid 432 through 448 Processing helix chain 'B' and resid 455 through 478 Processing helix chain 'B' and resid 490 through 499 Processing helix chain 'B' and resid 501 through 528 removed outlier: 3.771A pdb=" N ILE B 505 " --> pdb=" O SER B 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 553 Processing helix chain 'C' and resid 65 through 89 removed outlier: 3.630A pdb=" N VAL C 86 " --> pdb=" O GLU C 82 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N GLU C 87 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 94 removed outlier: 3.612A pdb=" N SER C 94 " --> pdb=" O ARG C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 110 Processing helix chain 'C' and resid 157 through 175 removed outlier: 3.658A pdb=" N VAL C 175 " --> pdb=" O LYS C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 212 Processing helix chain 'C' and resid 229 through 244 removed outlier: 3.736A pdb=" N MET C 233 " --> pdb=" O GLY C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 249 through 254 Processing helix chain 'C' and resid 259 through 263 Processing helix chain 'C' and resid 267 through 285 removed outlier: 4.414A pdb=" N THR C 272 " --> pdb=" O ARG C 268 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N GLY C 273 " --> pdb=" O ILE C 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 294 removed outlier: 3.559A pdb=" N MET C 290 " --> pdb=" O GLU C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 310 through 324 Processing helix chain 'C' and resid 344 through 356 Processing helix chain 'C' and resid 370 through 374 Processing helix chain 'C' and resid 391 through 396 removed outlier: 3.909A pdb=" N ARG C 395 " --> pdb=" O SER C 391 " (cutoff:3.500A) Processing helix chain 'C' and resid 410 through 421 Processing helix chain 'C' and resid 426 through 431 Processing helix chain 'C' and resid 432 through 448 Processing helix chain 'C' and resid 455 through 478 Processing helix chain 'C' and resid 490 through 499 Processing helix chain 'C' and resid 501 through 528 removed outlier: 3.772A pdb=" N ILE C 505 " --> pdb=" O SER C 501 " (cutoff:3.500A) Processing helix chain 'C' and resid 533 through 553 Processing helix chain 'D' and resid 65 through 89 removed outlier: 3.630A pdb=" N VAL D 86 " --> pdb=" O GLU D 82 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N GLU D 87 " --> pdb=" O ASP D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 94 removed outlier: 3.612A pdb=" N SER D 94 " --> pdb=" O ARG D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 110 Processing helix chain 'D' and resid 157 through 175 removed outlier: 3.658A pdb=" N VAL D 175 " --> pdb=" O LYS D 171 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 212 Processing helix chain 'D' and resid 229 through 244 removed outlier: 3.735A pdb=" N MET D 233 " --> pdb=" O GLY D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 254 Processing helix chain 'D' and resid 259 through 263 Processing helix chain 'D' and resid 267 through 285 removed outlier: 4.415A pdb=" N THR D 272 " --> pdb=" O ARG D 268 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N GLY D 273 " --> pdb=" O ILE D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 294 removed outlier: 3.561A pdb=" N MET D 290 " --> pdb=" O GLU D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 310 through 324 Processing helix chain 'D' and resid 344 through 356 Processing helix chain 'D' and resid 370 through 374 Processing helix chain 'D' and resid 391 through 396 removed outlier: 3.910A pdb=" N ARG D 395 " --> pdb=" O SER D 391 " (cutoff:3.500A) Processing helix chain 'D' and resid 410 through 421 Processing helix chain 'D' and resid 426 through 431 Processing helix chain 'D' and resid 432 through 448 Processing helix chain 'D' and resid 455 through 478 Processing helix chain 'D' and resid 490 through 499 Processing helix chain 'D' and resid 501 through 528 removed outlier: 3.771A pdb=" N ILE D 505 " --> pdb=" O SER D 501 " (cutoff:3.500A) Processing helix chain 'D' and resid 533 through 553 Processing helix chain 'E' and resid 65 through 89 removed outlier: 3.630A pdb=" N VAL E 86 " --> pdb=" O GLU E 82 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N GLU E 87 " --> pdb=" O ASP E 83 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 94 removed outlier: 3.611A pdb=" N SER E 94 " --> pdb=" O ARG E 90 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 110 Processing helix chain 'E' and resid 157 through 175 removed outlier: 3.659A pdb=" N VAL E 175 " --> pdb=" O LYS E 171 " (cutoff:3.500A) Processing helix chain 'E' and resid 194 through 212 Processing helix chain 'E' and resid 229 through 244 removed outlier: 3.735A pdb=" N MET E 233 " --> pdb=" O GLY E 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 249 through 254 Processing helix chain 'E' and resid 259 through 263 Processing helix chain 'E' and resid 267 through 285 removed outlier: 4.414A pdb=" N THR E 272 " --> pdb=" O ARG E 268 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N GLY E 273 " --> pdb=" O ILE E 269 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 294 removed outlier: 3.560A pdb=" N MET E 290 " --> pdb=" O GLU E 286 " (cutoff:3.500A) Processing helix chain 'E' and resid 310 through 324 Processing helix chain 'E' and resid 344 through 356 Processing helix chain 'E' and resid 370 through 374 Processing helix chain 'E' and resid 391 through 396 removed outlier: 3.911A pdb=" N ARG E 395 " --> pdb=" O SER E 391 " (cutoff:3.500A) Processing helix chain 'E' and resid 410 through 421 Processing helix chain 'E' and resid 426 through 431 Processing helix chain 'E' and resid 432 through 448 Processing helix chain 'E' and resid 455 through 478 Processing helix chain 'E' and resid 490 through 499 Processing helix chain 'E' and resid 501 through 528 removed outlier: 3.772A pdb=" N ILE E 505 " --> pdb=" O SER E 501 " (cutoff:3.500A) Processing helix chain 'E' and resid 533 through 553 Processing helix chain 'F' and resid 65 through 89 removed outlier: 3.630A pdb=" N VAL F 86 " --> pdb=" O GLU F 82 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N GLU F 87 " --> pdb=" O ASP F 83 " (cutoff:3.500A) Processing helix chain 'F' and resid 89 through 94 removed outlier: 3.612A pdb=" N SER F 94 " --> pdb=" O ARG F 90 " (cutoff:3.500A) Processing helix chain 'F' and resid 98 through 110 Processing helix chain 'F' and resid 157 through 175 removed outlier: 3.658A pdb=" N VAL F 175 " --> pdb=" O LYS F 171 " (cutoff:3.500A) Processing helix chain 'F' and resid 194 through 212 Processing helix chain 'F' and resid 229 through 244 removed outlier: 3.736A pdb=" N MET F 233 " --> pdb=" O GLY F 229 " (cutoff:3.500A) Processing helix chain 'F' and resid 249 through 254 Processing helix chain 'F' and resid 259 through 263 Processing helix chain 'F' and resid 267 through 285 removed outlier: 4.413A pdb=" N THR F 272 " --> pdb=" O ARG F 268 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N GLY F 273 " --> pdb=" O ILE F 269 " (cutoff:3.500A) Processing helix chain 'F' and resid 286 through 294 removed outlier: 3.560A pdb=" N MET F 290 " --> pdb=" O GLU F 286 " (cutoff:3.500A) Processing helix chain 'F' and resid 310 through 324 Processing helix chain 'F' and resid 344 through 356 Processing helix chain 'F' and resid 370 through 374 Processing helix chain 'F' and resid 391 through 396 removed outlier: 3.910A pdb=" N ARG F 395 " --> pdb=" O SER F 391 " (cutoff:3.500A) Processing helix chain 'F' and resid 410 through 421 Processing helix chain 'F' and resid 426 through 431 Processing helix chain 'F' and resid 432 through 448 Processing helix chain 'F' and resid 455 through 478 Processing helix chain 'F' and resid 490 through 499 Processing helix chain 'F' and resid 501 through 528 removed outlier: 3.772A pdb=" N ILE F 505 " --> pdb=" O SER F 501 " (cutoff:3.500A) Processing helix chain 'F' and resid 533 through 553 Processing sheet with id=AA1, first strand: chain 'A' and resid 220 through 224 removed outlier: 3.687A pdb=" N GLY A 149 " --> pdb=" O ALA A 182 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLY E 149 " --> pdb=" O ALA E 182 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 365 through 366 removed outlier: 6.693A pdb=" N PHE A 304 " --> pdb=" O ALA A 329 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N GLY A 331 " --> pdb=" O PHE A 304 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N VAL A 306 " --> pdb=" O GLY A 331 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N LEU A 379 " --> pdb=" O ALA A 402 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N ILE A 401 " --> pdb=" O ILE A 425 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 220 through 224 removed outlier: 3.687A pdb=" N GLY B 149 " --> pdb=" O ALA B 182 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLY D 149 " --> pdb=" O ALA D 182 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 365 through 366 removed outlier: 6.692A pdb=" N PHE B 304 " --> pdb=" O ALA B 329 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N GLY B 331 " --> pdb=" O PHE B 304 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N VAL B 306 " --> pdb=" O GLY B 331 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N LEU B 379 " --> pdb=" O ALA B 402 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ILE B 401 " --> pdb=" O ILE B 425 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 220 through 224 removed outlier: 3.688A pdb=" N GLY C 149 " --> pdb=" O ALA C 182 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLY F 149 " --> pdb=" O ALA F 182 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 365 through 366 removed outlier: 6.693A pdb=" N PHE C 304 " --> pdb=" O ALA C 329 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N GLY C 331 " --> pdb=" O PHE C 304 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N VAL C 306 " --> pdb=" O GLY C 331 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N LEU C 379 " --> pdb=" O ALA C 402 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ILE C 401 " --> pdb=" O ILE C 425 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 365 through 366 removed outlier: 6.692A pdb=" N PHE D 304 " --> pdb=" O ALA D 329 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N GLY D 331 " --> pdb=" O PHE D 304 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N VAL D 306 " --> pdb=" O GLY D 331 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N LEU D 379 " --> pdb=" O ALA D 402 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N ILE D 401 " --> pdb=" O ILE D 425 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 365 through 366 removed outlier: 6.693A pdb=" N PHE E 304 " --> pdb=" O ALA E 329 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N GLY E 331 " --> pdb=" O PHE E 304 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N VAL E 306 " --> pdb=" O GLY E 331 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N LEU E 379 " --> pdb=" O ALA E 402 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N ILE E 401 " --> pdb=" O ILE E 425 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 365 through 366 removed outlier: 6.693A pdb=" N PHE F 304 " --> pdb=" O ALA F 329 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N GLY F 331 " --> pdb=" O PHE F 304 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N VAL F 306 " --> pdb=" O GLY F 331 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N LEU F 379 " --> pdb=" O ALA F 402 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N ILE F 401 " --> pdb=" O ILE F 425 " (cutoff:3.500A) 1416 hydrogen bonds defined for protein. 4050 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.53 Time building geometry restraints manager: 2.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7631 1.34 - 1.46: 3653 1.46 - 1.58: 11767 1.58 - 1.70: 0 1.70 - 1.81: 180 Bond restraints: 23231 Sorted by residual: bond pdb=" C THR C 144 " pdb=" N PRO C 145 " ideal model delta sigma weight residual 1.333 1.360 -0.027 1.01e-02 9.80e+03 6.96e+00 bond pdb=" C THR F 144 " pdb=" N PRO F 145 " ideal model delta sigma weight residual 1.333 1.360 -0.026 1.01e-02 9.80e+03 6.78e+00 bond pdb=" C THR E 144 " pdb=" N PRO E 145 " ideal model delta sigma weight residual 1.333 1.360 -0.026 1.01e-02 9.80e+03 6.69e+00 bond pdb=" C THR B 144 " pdb=" N PRO B 145 " ideal model delta sigma weight residual 1.333 1.360 -0.026 1.01e-02 9.80e+03 6.63e+00 bond pdb=" C THR A 144 " pdb=" N PRO A 145 " ideal model delta sigma weight residual 1.333 1.359 -0.025 1.01e-02 9.80e+03 6.23e+00 ... (remaining 23226 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.33: 31042 2.33 - 4.66: 317 4.66 - 6.99: 30 6.99 - 9.32: 18 9.32 - 11.65: 6 Bond angle restraints: 31413 Sorted by residual: angle pdb=" N HIS F 142 " pdb=" CA HIS F 142 " pdb=" C HIS F 142 " ideal model delta sigma weight residual 111.07 102.28 8.79 1.07e+00 8.73e-01 6.75e+01 angle pdb=" N HIS C 142 " pdb=" CA HIS C 142 " pdb=" C HIS C 142 " ideal model delta sigma weight residual 111.07 102.37 8.70 1.07e+00 8.73e-01 6.61e+01 angle pdb=" N HIS B 142 " pdb=" CA HIS B 142 " pdb=" C HIS B 142 " ideal model delta sigma weight residual 111.07 102.56 8.51 1.07e+00 8.73e-01 6.32e+01 angle pdb=" N HIS E 142 " pdb=" CA HIS E 142 " pdb=" C HIS E 142 " ideal model delta sigma weight residual 111.07 102.61 8.46 1.07e+00 8.73e-01 6.25e+01 angle pdb=" N HIS D 142 " pdb=" CA HIS D 142 " pdb=" C HIS D 142 " ideal model delta sigma weight residual 111.28 102.99 8.29 1.09e+00 8.42e-01 5.79e+01 ... (remaining 31408 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.11: 12662 16.11 - 32.21: 1032 32.21 - 48.32: 152 48.32 - 64.42: 42 64.42 - 80.52: 18 Dihedral angle restraints: 13906 sinusoidal: 5482 harmonic: 8424 Sorted by residual: dihedral pdb=" CA SER F 270 " pdb=" C SER F 270 " pdb=" N ALA F 271 " pdb=" CA ALA F 271 " ideal model delta harmonic sigma weight residual -180.00 -163.06 -16.94 0 5.00e+00 4.00e-02 1.15e+01 dihedral pdb=" CA SER D 270 " pdb=" C SER D 270 " pdb=" N ALA D 271 " pdb=" CA ALA D 271 " ideal model delta harmonic sigma weight residual -180.00 -163.07 -16.93 0 5.00e+00 4.00e-02 1.15e+01 dihedral pdb=" CA SER B 270 " pdb=" C SER B 270 " pdb=" N ALA B 271 " pdb=" CA ALA B 271 " ideal model delta harmonic sigma weight residual -180.00 -163.09 -16.91 0 5.00e+00 4.00e-02 1.14e+01 ... (remaining 13903 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 2782 0.054 - 0.107: 555 0.107 - 0.161: 79 0.161 - 0.215: 4 0.215 - 0.268: 12 Chirality restraints: 3432 Sorted by residual: chirality pdb=" CA GLU D 552 " pdb=" N GLU D 552 " pdb=" C GLU D 552 " pdb=" CB GLU D 552 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" CA GLU A 552 " pdb=" N GLU A 552 " pdb=" C GLU A 552 " pdb=" CB GLU A 552 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" CB ILE C 401 " pdb=" CA ILE C 401 " pdb=" CG1 ILE C 401 " pdb=" CG2 ILE C 401 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.57e+00 ... (remaining 3429 not shown) Planarity restraints: 4121 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN D 141 " -0.009 2.00e-02 2.50e+03 1.85e-02 3.43e+00 pdb=" C GLN D 141 " 0.032 2.00e-02 2.50e+03 pdb=" O GLN D 141 " -0.012 2.00e-02 2.50e+03 pdb=" N HIS D 142 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 141 " 0.009 2.00e-02 2.50e+03 1.84e-02 3.38e+00 pdb=" C GLN A 141 " -0.032 2.00e-02 2.50e+03 pdb=" O GLN A 141 " 0.012 2.00e-02 2.50e+03 pdb=" N HIS A 142 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS B 258 " -0.029 5.00e-02 4.00e+02 4.47e-02 3.20e+00 pdb=" N PRO B 259 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO B 259 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 259 " -0.025 5.00e-02 4.00e+02 ... (remaining 4118 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 7478 2.84 - 3.36: 23379 3.36 - 3.87: 38561 3.87 - 4.39: 43906 4.39 - 4.90: 73975 Nonbonded interactions: 187299 Sorted by model distance: nonbonded pdb=" OD1 ASN E 392 " pdb=" NH2 ARG E 395 " model vdw 2.329 3.120 nonbonded pdb=" OD1 ASN C 392 " pdb=" NH2 ARG C 395 " model vdw 2.329 3.120 nonbonded pdb=" OD1 ASN D 392 " pdb=" NH2 ARG D 395 " model vdw 2.329 3.120 nonbonded pdb=" OD1 ASN F 392 " pdb=" NH2 ARG F 395 " model vdw 2.329 3.120 nonbonded pdb=" OD1 ASN A 392 " pdb=" NH2 ARG A 395 " model vdw 2.330 3.120 ... (remaining 187294 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 63 through 360 or (resid 361 and (name N or name CA or nam \ e C or name O or name CB )) or resid 362 through 556)) selection = (chain 'B' and (resid 63 through 360 or (resid 361 and (name N or name CA or nam \ e C or name O or name CB )) or resid 362 through 556)) selection = (chain 'C' and (resid 63 through 360 or (resid 361 and (name N or name CA or nam \ e C or name O or name CB )) or resid 362 through 556)) selection = (chain 'D' and (resid 63 through 360 or (resid 361 and (name N or name CA or nam \ e C or name O or name CB )) or resid 362 through 556)) selection = (chain 'E' and (resid 63 through 360 or (resid 361 and (name N or name CA or nam \ e C or name O or name CB )) or resid 362 through 556)) selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 22.480 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6782 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 23231 Z= 0.158 Angle : 0.636 11.648 31413 Z= 0.381 Chirality : 0.044 0.268 3432 Planarity : 0.004 0.045 4121 Dihedral : 12.389 80.525 8542 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.59 (0.15), residues: 2952 helix: 2.27 (0.13), residues: 1542 sheet: 0.11 (0.25), residues: 372 loop : -0.43 (0.18), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 101 TYR 0.010 0.001 TYR B 240 PHE 0.017 0.002 PHE B 67 TRP 0.004 0.001 TRP C 338 HIS 0.003 0.001 HIS F 315 Details of bonding type rmsd covalent geometry : bond 0.00276 (23231) covalent geometry : angle 0.63644 (31413) hydrogen bonds : bond 0.14589 ( 1416) hydrogen bonds : angle 5.36260 ( 4050) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 612 residues out of total 2466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 612 time to evaluate : 0.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 314 LEU cc_start: 0.7857 (tp) cc_final: 0.7549 (tp) REVERT: A 326 LYS cc_start: 0.7187 (ptpp) cc_final: 0.6966 (ptmt) REVERT: A 349 GLU cc_start: 0.7468 (tm-30) cc_final: 0.7166 (mt-10) REVERT: A 412 GLU cc_start: 0.8731 (mm-30) cc_final: 0.8336 (pm20) REVERT: A 471 GLN cc_start: 0.7407 (tt0) cc_final: 0.6808 (tp40) REVERT: A 495 ASP cc_start: 0.7209 (m-30) cc_final: 0.6933 (m-30) REVERT: B 238 ASP cc_start: 0.7071 (t0) cc_final: 0.6845 (t0) REVERT: B 309 PHE cc_start: 0.4447 (t80) cc_final: 0.4074 (t80) REVERT: B 412 GLU cc_start: 0.8588 (mm-30) cc_final: 0.8305 (pm20) REVERT: B 468 MET cc_start: 0.6197 (ttp) cc_final: 0.5929 (ttp) REVERT: B 472 GLU cc_start: 0.7365 (mm-30) cc_final: 0.7047 (mm-30) REVERT: B 495 ASP cc_start: 0.7035 (m-30) cc_final: 0.6566 (m-30) REVERT: B 550 TYR cc_start: 0.8209 (t80) cc_final: 0.7896 (t80) REVERT: C 188 ILE cc_start: 0.7507 (tp) cc_final: 0.7095 (tp) REVERT: C 204 ARG cc_start: 0.8261 (mmm160) cc_final: 0.7822 (tpt90) REVERT: C 215 ILE cc_start: 0.8551 (tt) cc_final: 0.8331 (tt) REVERT: C 314 LEU cc_start: 0.8258 (tp) cc_final: 0.7845 (tp) REVERT: C 349 GLU cc_start: 0.7608 (tm-30) cc_final: 0.7251 (mt-10) REVERT: C 412 GLU cc_start: 0.8627 (mm-30) cc_final: 0.8416 (pm20) REVERT: C 495 ASP cc_start: 0.7209 (m-30) cc_final: 0.6913 (m-30) REVERT: D 258 LYS cc_start: 0.7355 (mttt) cc_final: 0.7119 (mtpp) REVERT: D 314 LEU cc_start: 0.7761 (tp) cc_final: 0.7328 (tp) REVERT: D 349 GLU cc_start: 0.7455 (tm-30) cc_final: 0.7147 (mt-10) REVERT: D 412 GLU cc_start: 0.8761 (mm-30) cc_final: 0.8494 (pm20) REVERT: D 471 GLN cc_start: 0.7496 (tt0) cc_final: 0.6905 (tp40) REVERT: D 495 ASP cc_start: 0.7221 (m-30) cc_final: 0.6962 (m-30) REVERT: E 170 TYR cc_start: 0.7181 (m-10) cc_final: 0.6969 (m-10) REVERT: E 238 ASP cc_start: 0.7103 (t0) cc_final: 0.6885 (t0) REVERT: E 309 PHE cc_start: 0.4480 (t80) cc_final: 0.4105 (t80) REVERT: E 317 MET cc_start: 0.6802 (ptm) cc_final: 0.6596 (ptt) REVERT: E 412 GLU cc_start: 0.8581 (mm-30) cc_final: 0.8288 (pm20) REVERT: E 495 ASP cc_start: 0.6955 (m-30) cc_final: 0.6584 (m-30) REVERT: E 550 TYR cc_start: 0.8195 (t80) cc_final: 0.7893 (t80) REVERT: F 188 ILE cc_start: 0.7585 (tp) cc_final: 0.7260 (tp) REVERT: F 204 ARG cc_start: 0.8207 (mmm160) cc_final: 0.7927 (tpt90) REVERT: F 215 ILE cc_start: 0.8559 (tt) cc_final: 0.8332 (tt) REVERT: F 314 LEU cc_start: 0.8252 (tp) cc_final: 0.7856 (tp) REVERT: F 317 MET cc_start: 0.6908 (ptm) cc_final: 0.6707 (ptt) REVERT: F 347 GLU cc_start: 0.8831 (mt-10) cc_final: 0.8564 (tm-30) REVERT: F 349 GLU cc_start: 0.7450 (tm-30) cc_final: 0.7131 (mt-10) REVERT: F 412 GLU cc_start: 0.8658 (mm-30) cc_final: 0.8375 (mp0) REVERT: F 495 ASP cc_start: 0.7232 (m-30) cc_final: 0.6992 (m-30) outliers start: 0 outliers final: 0 residues processed: 612 average time/residue: 0.1868 time to fit residues: 171.0443 Evaluate side-chains 362 residues out of total 2466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 362 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 0.0970 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 0.6980 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 GLN B 262 GLN ** B 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 421 ASN ** B 507 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 262 GLN D 262 GLN E 262 GLN ** E 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 421 ASN ** E 507 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 262 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.186003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.143609 restraints weight = 29129.960| |-----------------------------------------------------------------------------| r_work (start): 0.3688 rms_B_bonded: 2.67 r_work: 0.3486 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 23231 Z= 0.128 Angle : 0.560 9.812 31413 Z= 0.293 Chirality : 0.044 0.203 3432 Planarity : 0.004 0.034 4121 Dihedral : 4.249 15.747 3228 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 2.23 % Allowed : 10.21 % Favored : 87.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.62 (0.16), residues: 2952 helix: 2.33 (0.13), residues: 1590 sheet: 0.25 (0.25), residues: 366 loop : -0.70 (0.19), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 99 TYR 0.017 0.001 TYR D 528 PHE 0.028 0.002 PHE C 304 TRP 0.007 0.001 TRP B 338 HIS 0.006 0.001 HIS F 507 Details of bonding type rmsd covalent geometry : bond 0.00289 (23231) covalent geometry : angle 0.56039 (31413) hydrogen bonds : bond 0.04319 ( 1416) hydrogen bonds : angle 4.06328 ( 4050) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 2466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 399 time to evaluate : 0.886 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 262 GLN cc_start: 0.8262 (OUTLIER) cc_final: 0.7526 (mm110) REVERT: A 266 HIS cc_start: 0.7481 (OUTLIER) cc_final: 0.6968 (m-70) REVERT: A 281 GLU cc_start: 0.7809 (tp30) cc_final: 0.7331 (tp30) REVERT: A 314 LEU cc_start: 0.8068 (tp) cc_final: 0.7838 (tp) REVERT: A 338 TRP cc_start: 0.7692 (t-100) cc_final: 0.7372 (t-100) REVERT: A 373 GLU cc_start: 0.7151 (mp0) cc_final: 0.6947 (mp0) REVERT: A 399 LYS cc_start: 0.7782 (mmmt) cc_final: 0.7071 (mttm) REVERT: A 495 ASP cc_start: 0.7851 (m-30) cc_final: 0.7605 (m-30) REVERT: B 143 ARG cc_start: 0.8148 (mmm160) cc_final: 0.6427 (mpt-90) REVERT: B 262 GLN cc_start: 0.8145 (OUTLIER) cc_final: 0.7939 (mp10) REVERT: B 326 LYS cc_start: 0.7910 (mtpt) cc_final: 0.7143 (mttp) REVERT: B 349 GLU cc_start: 0.7515 (tm-30) cc_final: 0.7072 (mp0) REVERT: B 399 LYS cc_start: 0.7755 (mmmt) cc_final: 0.7437 (mttm) REVERT: B 468 MET cc_start: 0.7333 (ttp) cc_final: 0.7075 (ttp) REVERT: B 472 GLU cc_start: 0.7965 (mm-30) cc_final: 0.7561 (mm-30) REVERT: B 495 ASP cc_start: 0.7695 (m-30) cc_final: 0.7216 (m-30) REVERT: C 207 MET cc_start: 0.8218 (mtm) cc_final: 0.7969 (mtm) REVERT: C 281 GLU cc_start: 0.7597 (tp30) cc_final: 0.7260 (tp30) REVERT: C 282 ASN cc_start: 0.8227 (m-40) cc_final: 0.7967 (t0) REVERT: C 349 GLU cc_start: 0.7535 (tm-30) cc_final: 0.7283 (mt-10) REVERT: C 373 GLU cc_start: 0.7416 (mp0) cc_final: 0.6987 (mp0) REVERT: C 399 LYS cc_start: 0.7632 (mmmt) cc_final: 0.7014 (mttm) REVERT: C 472 GLU cc_start: 0.7901 (mm-30) cc_final: 0.7544 (mm-30) REVERT: C 495 ASP cc_start: 0.7970 (m-30) cc_final: 0.7721 (m-30) REVERT: D 266 HIS cc_start: 0.7494 (OUTLIER) cc_final: 0.6991 (m-70) REVERT: D 281 GLU cc_start: 0.7469 (tp30) cc_final: 0.6949 (tp30) REVERT: D 282 ASN cc_start: 0.8160 (m-40) cc_final: 0.7888 (m110) REVERT: D 338 TRP cc_start: 0.7722 (t-100) cc_final: 0.7504 (t-100) REVERT: D 349 GLU cc_start: 0.7440 (tm-30) cc_final: 0.7233 (mt-10) REVERT: D 399 LYS cc_start: 0.7868 (mmmt) cc_final: 0.7092 (mttt) REVERT: D 495 ASP cc_start: 0.7765 (m-30) cc_final: 0.7449 (m-30) REVERT: E 143 ARG cc_start: 0.8167 (mmm160) cc_final: 0.6455 (mpt-90) REVERT: E 349 GLU cc_start: 0.7549 (tm-30) cc_final: 0.7075 (mp0) REVERT: E 399 LYS cc_start: 0.7771 (mmmt) cc_final: 0.7450 (mttm) REVERT: E 472 GLU cc_start: 0.7961 (mm-30) cc_final: 0.7568 (mm-30) REVERT: E 495 ASP cc_start: 0.7774 (m-30) cc_final: 0.7297 (m-30) REVERT: F 207 MET cc_start: 0.8238 (mtm) cc_final: 0.7981 (mtm) REVERT: F 281 GLU cc_start: 0.7593 (tp30) cc_final: 0.7280 (tp30) REVERT: F 282 ASN cc_start: 0.8217 (m-40) cc_final: 0.7963 (t0) REVERT: F 295 MET cc_start: 0.6724 (ptp) cc_final: 0.6460 (ptm) REVERT: F 314 LEU cc_start: 0.8271 (tp) cc_final: 0.7904 (tp) REVERT: F 347 GLU cc_start: 0.8799 (mt-10) cc_final: 0.8574 (tm-30) REVERT: F 349 GLU cc_start: 0.7502 (tm-30) cc_final: 0.7240 (mt-10) REVERT: F 373 GLU cc_start: 0.7495 (mp0) cc_final: 0.7074 (mp0) REVERT: F 399 LYS cc_start: 0.7431 (mmmt) cc_final: 0.6713 (mttm) REVERT: F 472 GLU cc_start: 0.7874 (mm-30) cc_final: 0.7571 (mm-30) outliers start: 53 outliers final: 18 residues processed: 427 average time/residue: 0.1770 time to fit residues: 116.2231 Evaluate side-chains 367 residues out of total 2466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 345 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 GLN Chi-restraints excluded: chain A residue 266 HIS Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain B residue 262 GLN Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 450 SER Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain C residue 296 THR Chi-restraints excluded: chain C residue 449 VAL Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain D residue 266 HIS Chi-restraints excluded: chain D residue 291 SER Chi-restraints excluded: chain D residue 462 SER Chi-restraints excluded: chain D residue 490 THR Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain E residue 490 THR Chi-restraints excluded: chain F residue 296 THR Chi-restraints excluded: chain F residue 418 LEU Chi-restraints excluded: chain F residue 449 VAL Chi-restraints excluded: chain F residue 490 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 15 optimal weight: 0.0170 chunk 98 optimal weight: 9.9990 chunk 257 optimal weight: 0.0070 chunk 152 optimal weight: 0.8980 chunk 90 optimal weight: 0.9990 chunk 151 optimal weight: 0.8980 chunk 75 optimal weight: 0.9990 chunk 262 optimal weight: 4.9990 chunk 226 optimal weight: 0.9990 chunk 103 optimal weight: 0.0270 chunk 280 optimal weight: 8.9990 overall best weight: 0.3694 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 262 GLN D 315 HIS ** E 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 507 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 262 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.185407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.143536 restraints weight = 29201.248| |-----------------------------------------------------------------------------| r_work (start): 0.3703 rms_B_bonded: 2.40 r_work: 0.3535 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3373 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.2613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 23231 Z= 0.106 Angle : 0.522 11.179 31413 Z= 0.266 Chirality : 0.042 0.172 3432 Planarity : 0.004 0.034 4121 Dihedral : 4.031 19.587 3228 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 1.97 % Allowed : 13.78 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.60 (0.15), residues: 2952 helix: 2.38 (0.13), residues: 1590 sheet: 0.28 (0.26), residues: 366 loop : -0.84 (0.18), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 76 TYR 0.015 0.001 TYR B 528 PHE 0.027 0.002 PHE C 304 TRP 0.016 0.001 TRP E 338 HIS 0.008 0.001 HIS A 142 Details of bonding type rmsd covalent geometry : bond 0.00246 (23231) covalent geometry : angle 0.52185 (31413) hydrogen bonds : bond 0.03728 ( 1416) hydrogen bonds : angle 3.86779 ( 4050) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 2466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 370 time to evaluate : 0.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 PHE cc_start: 0.6600 (m-10) cc_final: 0.5694 (m-10) REVERT: A 143 ARG cc_start: 0.8252 (mmm160) cc_final: 0.6419 (mpt-90) REVERT: A 266 HIS cc_start: 0.7471 (OUTLIER) cc_final: 0.7084 (m-70) REVERT: A 281 GLU cc_start: 0.7848 (tp30) cc_final: 0.7397 (tp30) REVERT: A 282 ASN cc_start: 0.8369 (m-40) cc_final: 0.7831 (m110) REVERT: A 326 LYS cc_start: 0.8278 (mttp) cc_final: 0.7506 (ptmt) REVERT: A 338 TRP cc_start: 0.7624 (t-100) cc_final: 0.7251 (t-100) REVERT: A 399 LYS cc_start: 0.7773 (mmmt) cc_final: 0.7250 (mttm) REVERT: A 495 ASP cc_start: 0.7964 (m-30) cc_final: 0.7691 (m-30) REVERT: A 549 VAL cc_start: 0.7792 (t) cc_final: 0.7558 (t) REVERT: B 143 ARG cc_start: 0.8147 (mmm160) cc_final: 0.6544 (mpt-90) REVERT: B 262 GLN cc_start: 0.7846 (mm-40) cc_final: 0.6956 (mp10) REVERT: B 282 ASN cc_start: 0.8228 (m-40) cc_final: 0.7808 (m110) REVERT: B 326 LYS cc_start: 0.7874 (mtpt) cc_final: 0.7492 (mtpt) REVERT: B 399 LYS cc_start: 0.7833 (mmmt) cc_final: 0.7589 (mttm) REVERT: B 468 MET cc_start: 0.7488 (ttp) cc_final: 0.7222 (ttp) REVERT: B 472 GLU cc_start: 0.8043 (mm-30) cc_final: 0.7630 (mm-30) REVERT: B 495 ASP cc_start: 0.7800 (m-30) cc_final: 0.7324 (m-30) REVERT: C 207 MET cc_start: 0.8447 (mtm) cc_final: 0.8239 (mtm) REVERT: C 281 GLU cc_start: 0.7695 (tp30) cc_final: 0.7378 (tp30) REVERT: C 282 ASN cc_start: 0.8392 (m-40) cc_final: 0.8027 (t0) REVERT: C 349 GLU cc_start: 0.7513 (tm-30) cc_final: 0.7255 (mt-10) REVERT: C 373 GLU cc_start: 0.7204 (mp0) cc_final: 0.6877 (mp0) REVERT: C 399 LYS cc_start: 0.7658 (mmmt) cc_final: 0.7190 (mttm) REVERT: C 472 GLU cc_start: 0.8110 (mm-30) cc_final: 0.7733 (mm-30) REVERT: C 495 ASP cc_start: 0.8062 (m-30) cc_final: 0.7855 (m-30) REVERT: D 66 PHE cc_start: 0.5752 (OUTLIER) cc_final: 0.5341 (m-10) REVERT: D 67 PHE cc_start: 0.6612 (m-10) cc_final: 0.5868 (m-10) REVERT: D 143 ARG cc_start: 0.8203 (mmm160) cc_final: 0.6359 (mpt-90) REVERT: D 266 HIS cc_start: 0.7518 (OUTLIER) cc_final: 0.7258 (m-70) REVERT: D 281 GLU cc_start: 0.7511 (tp30) cc_final: 0.7113 (tp30) REVERT: D 282 ASN cc_start: 0.8380 (m-40) cc_final: 0.7945 (m110) REVERT: D 326 LYS cc_start: 0.8364 (mttp) cc_final: 0.7533 (ptmt) REVERT: D 338 TRP cc_start: 0.7719 (t-100) cc_final: 0.7442 (t-100) REVERT: D 349 GLU cc_start: 0.7448 (tm-30) cc_final: 0.7223 (mt-10) REVERT: D 370 SER cc_start: 0.6974 (OUTLIER) cc_final: 0.6452 (t) REVERT: D 373 GLU cc_start: 0.7330 (mp0) cc_final: 0.7035 (pm20) REVERT: D 399 LYS cc_start: 0.7843 (mmmt) cc_final: 0.7268 (mttt) REVERT: D 495 ASP cc_start: 0.7961 (m-30) cc_final: 0.7692 (m-30) REVERT: D 514 MET cc_start: 0.9170 (mmp) cc_final: 0.8969 (mmt) REVERT: E 141 GLN cc_start: 0.7551 (OUTLIER) cc_final: 0.6987 (tp40) REVERT: E 143 ARG cc_start: 0.8180 (mmm160) cc_final: 0.6537 (mpt-90) REVERT: E 349 GLU cc_start: 0.7491 (tm-30) cc_final: 0.7112 (mp0) REVERT: E 399 LYS cc_start: 0.7841 (mmmt) cc_final: 0.7606 (mttm) REVERT: E 472 GLU cc_start: 0.8086 (mm-30) cc_final: 0.7685 (mm-30) REVERT: E 495 ASP cc_start: 0.7841 (m-30) cc_final: 0.7374 (m-30) REVERT: F 188 ILE cc_start: 0.8031 (tp) cc_final: 0.7829 (tp) REVERT: F 207 MET cc_start: 0.8421 (mtm) cc_final: 0.8149 (mtm) REVERT: F 281 GLU cc_start: 0.7693 (tp30) cc_final: 0.7353 (tp30) REVERT: F 282 ASN cc_start: 0.8381 (m-40) cc_final: 0.8001 (t0) REVERT: F 314 LEU cc_start: 0.8243 (tp) cc_final: 0.8035 (tp) REVERT: F 347 GLU cc_start: 0.8802 (mt-10) cc_final: 0.8581 (tm-30) REVERT: F 349 GLU cc_start: 0.7632 (tm-30) cc_final: 0.7329 (mt-10) REVERT: F 373 GLU cc_start: 0.7344 (mp0) cc_final: 0.7025 (mp0) REVERT: F 399 LYS cc_start: 0.7657 (mmmt) cc_final: 0.7290 (mttm) REVERT: F 472 GLU cc_start: 0.8030 (mm-30) cc_final: 0.7684 (mm-30) outliers start: 47 outliers final: 26 residues processed: 390 average time/residue: 0.1669 time to fit residues: 102.0425 Evaluate side-chains 361 residues out of total 2466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 330 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 266 HIS Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain B residue 66 PHE Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 450 SER Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 296 THR Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 449 VAL Chi-restraints excluded: chain D residue 66 PHE Chi-restraints excluded: chain D residue 266 HIS Chi-restraints excluded: chain D residue 295 MET Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 370 SER Chi-restraints excluded: chain D residue 490 THR Chi-restraints excluded: chain E residue 66 PHE Chi-restraints excluded: chain E residue 141 GLN Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain E residue 450 SER Chi-restraints excluded: chain E residue 490 THR Chi-restraints excluded: chain F residue 293 LEU Chi-restraints excluded: chain F residue 296 THR Chi-restraints excluded: chain F residue 306 VAL Chi-restraints excluded: chain F residue 418 LEU Chi-restraints excluded: chain F residue 449 VAL Chi-restraints excluded: chain F residue 490 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 41 optimal weight: 6.9990 chunk 16 optimal weight: 0.9980 chunk 128 optimal weight: 5.9990 chunk 273 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 153 optimal weight: 0.9990 chunk 190 optimal weight: 0.9990 chunk 67 optimal weight: 5.9990 chunk 230 optimal weight: 20.0000 chunk 213 optimal weight: 4.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 ASN A 262 GLN B 189 ASN B 262 GLN ** B 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 507 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 189 ASN C 262 GLN D 189 ASN E 189 ASN ** E 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 507 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 189 ASN F 262 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.177122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.135066 restraints weight = 29408.057| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 2.31 r_work: 0.3389 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.3235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 23231 Z= 0.156 Angle : 0.564 10.698 31413 Z= 0.291 Chirality : 0.045 0.190 3432 Planarity : 0.004 0.032 4121 Dihedral : 4.240 19.203 3228 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 3.74 % Allowed : 13.40 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.42 (0.15), residues: 2952 helix: 2.23 (0.13), residues: 1584 sheet: 0.25 (0.27), residues: 366 loop : -0.91 (0.18), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 99 TYR 0.013 0.002 TYR C 170 PHE 0.028 0.002 PHE C 304 TRP 0.017 0.001 TRP E 338 HIS 0.006 0.001 HIS A 142 Details of bonding type rmsd covalent geometry : bond 0.00377 (23231) covalent geometry : angle 0.56430 (31413) hydrogen bonds : bond 0.04420 ( 1416) hydrogen bonds : angle 3.98804 ( 4050) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 2466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 351 time to evaluate : 0.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 PHE cc_start: 0.6226 (m-10) cc_final: 0.5490 (m-10) REVERT: A 262 GLN cc_start: 0.8195 (OUTLIER) cc_final: 0.7973 (mp10) REVERT: A 266 HIS cc_start: 0.7254 (OUTLIER) cc_final: 0.6928 (m-70) REVERT: A 281 GLU cc_start: 0.7705 (tp30) cc_final: 0.7163 (tp30) REVERT: A 326 LYS cc_start: 0.8362 (mttp) cc_final: 0.7566 (ptmt) REVERT: A 338 TRP cc_start: 0.7580 (t-100) cc_final: 0.7221 (t-100) REVERT: A 370 SER cc_start: 0.6757 (OUTLIER) cc_final: 0.6157 (t) REVERT: A 373 GLU cc_start: 0.7305 (mp0) cc_final: 0.6773 (pm20) REVERT: A 387 GLN cc_start: 0.7000 (OUTLIER) cc_final: 0.6581 (mm110) REVERT: A 399 LYS cc_start: 0.7638 (mmmt) cc_final: 0.7108 (mttm) REVERT: A 495 ASP cc_start: 0.7871 (m-30) cc_final: 0.7428 (m-30) REVERT: B 67 PHE cc_start: 0.6460 (m-10) cc_final: 0.5639 (t80) REVERT: B 99 ARG cc_start: 0.7213 (mmm-85) cc_final: 0.6555 (mmm-85) REVERT: B 262 GLN cc_start: 0.8123 (OUTLIER) cc_final: 0.7752 (mp10) REVERT: B 282 ASN cc_start: 0.8195 (m-40) cc_final: 0.7695 (m110) REVERT: B 326 LYS cc_start: 0.7993 (mtpt) cc_final: 0.7691 (mtpt) REVERT: B 349 GLU cc_start: 0.7472 (tm-30) cc_final: 0.7192 (mt-10) REVERT: B 387 GLN cc_start: 0.6812 (OUTLIER) cc_final: 0.6427 (mm110) REVERT: B 472 GLU cc_start: 0.7990 (mm-30) cc_final: 0.7612 (mm-30) REVERT: B 495 ASP cc_start: 0.7784 (m-30) cc_final: 0.7243 (m-30) REVERT: C 67 PHE cc_start: 0.6327 (m-10) cc_final: 0.5591 (t80) REVERT: C 281 GLU cc_start: 0.7682 (tp30) cc_final: 0.7334 (tp30) REVERT: C 282 ASN cc_start: 0.8348 (m-40) cc_final: 0.7930 (m110) REVERT: C 295 MET cc_start: 0.7006 (OUTLIER) cc_final: 0.6683 (ptt) REVERT: C 349 GLU cc_start: 0.7463 (tm-30) cc_final: 0.7235 (mt-10) REVERT: C 387 GLN cc_start: 0.6940 (OUTLIER) cc_final: 0.6618 (mp10) REVERT: C 412 GLU cc_start: 0.7986 (pm20) cc_final: 0.7366 (tm-30) REVERT: D 67 PHE cc_start: 0.6277 (m-10) cc_final: 0.5521 (m-10) REVERT: D 233 MET cc_start: 0.8119 (mmm) cc_final: 0.7903 (mmt) REVERT: D 266 HIS cc_start: 0.7269 (OUTLIER) cc_final: 0.6941 (m-70) REVERT: D 282 ASN cc_start: 0.8212 (m-40) cc_final: 0.7840 (m110) REVERT: D 326 LYS cc_start: 0.8503 (mttp) cc_final: 0.7632 (ptmt) REVERT: D 338 TRP cc_start: 0.7666 (t-100) cc_final: 0.7363 (t-100) REVERT: D 370 SER cc_start: 0.7019 (OUTLIER) cc_final: 0.6152 (t) REVERT: D 373 GLU cc_start: 0.7058 (mp0) cc_final: 0.6846 (pm20) REVERT: D 399 LYS cc_start: 0.7765 (mmmt) cc_final: 0.7300 (mttt) REVERT: D 495 ASP cc_start: 0.7975 (m-30) cc_final: 0.7528 (m-30) REVERT: E 67 PHE cc_start: 0.6487 (m-10) cc_final: 0.5646 (t80) REVERT: E 282 ASN cc_start: 0.8189 (m-40) cc_final: 0.7715 (m110) REVERT: E 326 LYS cc_start: 0.7585 (mtpt) cc_final: 0.7357 (mtpt) REVERT: E 387 GLN cc_start: 0.6805 (OUTLIER) cc_final: 0.6433 (mm110) REVERT: E 399 LYS cc_start: 0.7950 (mmmt) cc_final: 0.7749 (mttm) REVERT: E 472 GLU cc_start: 0.8033 (mm-30) cc_final: 0.7668 (mm-30) REVERT: E 495 ASP cc_start: 0.7819 (m-30) cc_final: 0.7283 (m-30) REVERT: F 67 PHE cc_start: 0.6292 (m-10) cc_final: 0.5576 (t80) REVERT: F 207 MET cc_start: 0.8358 (mtm) cc_final: 0.8153 (mtm) REVERT: F 281 GLU cc_start: 0.7722 (tp30) cc_final: 0.7341 (tp30) REVERT: F 282 ASN cc_start: 0.8325 (m-40) cc_final: 0.7881 (m110) REVERT: F 314 LEU cc_start: 0.8499 (tp) cc_final: 0.8269 (tp) REVERT: F 347 GLU cc_start: 0.8813 (mt-10) cc_final: 0.8585 (tm-30) REVERT: F 349 GLU cc_start: 0.7585 (tm-30) cc_final: 0.7329 (mt-10) REVERT: F 387 GLN cc_start: 0.6893 (OUTLIER) cc_final: 0.6595 (mp10) outliers start: 89 outliers final: 58 residues processed: 406 average time/residue: 0.1584 time to fit residues: 103.0037 Evaluate side-chains 374 residues out of total 2466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 304 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 GLN Chi-restraints excluded: chain A residue 266 HIS Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 387 GLN Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 262 GLN Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 387 GLN Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain B residue 450 SER Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain C residue 262 GLN Chi-restraints excluded: chain C residue 295 MET Chi-restraints excluded: chain C residue 296 THR Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 380 ILE Chi-restraints excluded: chain C residue 387 GLN Chi-restraints excluded: chain C residue 430 LEU Chi-restraints excluded: chain C residue 449 VAL Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain D residue 207 MET Chi-restraints excluded: chain D residue 266 HIS Chi-restraints excluded: chain D residue 295 MET Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 370 SER Chi-restraints excluded: chain D residue 430 LEU Chi-restraints excluded: chain D residue 449 VAL Chi-restraints excluded: chain D residue 462 SER Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain D residue 490 THR Chi-restraints excluded: chain E residue 207 MET Chi-restraints excluded: chain E residue 215 ILE Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain E residue 387 GLN Chi-restraints excluded: chain E residue 424 VAL Chi-restraints excluded: chain E residue 430 LEU Chi-restraints excluded: chain E residue 449 VAL Chi-restraints excluded: chain E residue 450 SER Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain E residue 490 THR Chi-restraints excluded: chain F residue 262 GLN Chi-restraints excluded: chain F residue 296 THR Chi-restraints excluded: chain F residue 306 VAL Chi-restraints excluded: chain F residue 312 VAL Chi-restraints excluded: chain F residue 380 ILE Chi-restraints excluded: chain F residue 387 GLN Chi-restraints excluded: chain F residue 418 LEU Chi-restraints excluded: chain F residue 430 LEU Chi-restraints excluded: chain F residue 449 VAL Chi-restraints excluded: chain F residue 488 VAL Chi-restraints excluded: chain F residue 490 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 194 optimal weight: 1.9990 chunk 26 optimal weight: 8.9990 chunk 157 optimal weight: 0.6980 chunk 271 optimal weight: 9.9990 chunk 147 optimal weight: 10.0000 chunk 238 optimal weight: 2.9990 chunk 146 optimal weight: 0.9990 chunk 36 optimal weight: 0.0770 chunk 192 optimal weight: 0.7980 chunk 131 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 overall best weight: 0.9142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 262 GLN B 431 ASN C 262 GLN ** D 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 431 ASN E 262 GLN E 431 ASN F 262 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.178814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.140770 restraints weight = 29192.860| |-----------------------------------------------------------------------------| r_work (start): 0.3676 rms_B_bonded: 2.07 r_work: 0.3436 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.3431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 23231 Z= 0.125 Angle : 0.533 10.640 31413 Z= 0.272 Chirality : 0.043 0.158 3432 Planarity : 0.004 0.032 4121 Dihedral : 4.150 19.831 3228 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 3.65 % Allowed : 14.99 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.15), residues: 2952 helix: 2.22 (0.13), residues: 1596 sheet: 0.20 (0.27), residues: 366 loop : -0.89 (0.18), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 99 TYR 0.011 0.001 TYR B 528 PHE 0.033 0.002 PHE B 304 TRP 0.018 0.001 TRP E 338 HIS 0.003 0.001 HIS D 252 Details of bonding type rmsd covalent geometry : bond 0.00294 (23231) covalent geometry : angle 0.53330 (31413) hydrogen bonds : bond 0.03956 ( 1416) hydrogen bonds : angle 3.90502 ( 4050) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 2466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 324 time to evaluate : 0.890 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 PHE cc_start: 0.5894 (m-10) cc_final: 0.5352 (m-10) REVERT: A 266 HIS cc_start: 0.7295 (OUTLIER) cc_final: 0.7051 (m-70) REVERT: A 281 GLU cc_start: 0.7868 (tp30) cc_final: 0.7552 (tp30) REVERT: A 282 ASN cc_start: 0.8257 (m-40) cc_final: 0.7888 (m110) REVERT: A 326 LYS cc_start: 0.8244 (mttp) cc_final: 0.7601 (ptmt) REVERT: A 338 TRP cc_start: 0.7455 (t-100) cc_final: 0.7083 (t-100) REVERT: A 370 SER cc_start: 0.6846 (OUTLIER) cc_final: 0.6210 (t) REVERT: A 373 GLU cc_start: 0.7189 (mp0) cc_final: 0.6674 (pm20) REVERT: A 399 LYS cc_start: 0.7683 (mmmt) cc_final: 0.7266 (mttm) REVERT: A 495 ASP cc_start: 0.7921 (m-30) cc_final: 0.7519 (m-30) REVERT: A 549 VAL cc_start: 0.8385 (t) cc_final: 0.8121 (t) REVERT: B 67 PHE cc_start: 0.6005 (m-10) cc_final: 0.5745 (t80) REVERT: B 99 ARG cc_start: 0.7360 (mmm-85) cc_final: 0.6705 (mmm-85) REVERT: B 282 ASN cc_start: 0.8181 (m-40) cc_final: 0.7778 (m110) REVERT: B 326 LYS cc_start: 0.7952 (mtpt) cc_final: 0.7662 (mtpt) REVERT: B 387 GLN cc_start: 0.6894 (OUTLIER) cc_final: 0.6584 (mm110) REVERT: B 472 GLU cc_start: 0.8159 (mm-30) cc_final: 0.7870 (mm-30) REVERT: B 495 ASP cc_start: 0.7910 (m-30) cc_final: 0.7391 (m-30) REVERT: C 281 GLU cc_start: 0.7745 (tp30) cc_final: 0.7387 (tp30) REVERT: C 282 ASN cc_start: 0.8296 (m-40) cc_final: 0.7962 (m110) REVERT: C 295 MET cc_start: 0.7005 (OUTLIER) cc_final: 0.6691 (ptt) REVERT: C 387 GLN cc_start: 0.6983 (OUTLIER) cc_final: 0.6710 (mp10) REVERT: C 399 LYS cc_start: 0.7797 (mmmt) cc_final: 0.7424 (mttm) REVERT: D 67 PHE cc_start: 0.5911 (m-80) cc_final: 0.5440 (m-10) REVERT: D 266 HIS cc_start: 0.7329 (OUTLIER) cc_final: 0.7103 (m-70) REVERT: D 281 GLU cc_start: 0.7877 (tp30) cc_final: 0.7548 (tp30) REVERT: D 282 ASN cc_start: 0.8150 (m-40) cc_final: 0.7874 (m110) REVERT: D 326 LYS cc_start: 0.8336 (mttp) cc_final: 0.7619 (ptmt) REVERT: D 338 TRP cc_start: 0.7562 (t-100) cc_final: 0.7277 (t-100) REVERT: D 370 SER cc_start: 0.6962 (OUTLIER) cc_final: 0.6606 (t) REVERT: D 399 LYS cc_start: 0.7723 (mmmt) cc_final: 0.7303 (mttm) REVERT: D 495 ASP cc_start: 0.8020 (m-30) cc_final: 0.7587 (m-30) REVERT: D 549 VAL cc_start: 0.8401 (t) cc_final: 0.8135 (t) REVERT: E 67 PHE cc_start: 0.6036 (m-10) cc_final: 0.5755 (t80) REVERT: E 282 ASN cc_start: 0.8173 (m-40) cc_final: 0.7791 (m110) REVERT: E 326 LYS cc_start: 0.7696 (mtpt) cc_final: 0.7469 (mtpt) REVERT: E 387 GLN cc_start: 0.6825 (OUTLIER) cc_final: 0.6537 (mm110) REVERT: E 472 GLU cc_start: 0.8190 (mm-30) cc_final: 0.7895 (mm-30) REVERT: E 495 ASP cc_start: 0.7897 (m-30) cc_final: 0.7428 (m-30) REVERT: F 207 MET cc_start: 0.8324 (mtm) cc_final: 0.8079 (mtm) REVERT: F 281 GLU cc_start: 0.7756 (tp30) cc_final: 0.7435 (tp30) REVERT: F 282 ASN cc_start: 0.8299 (m-40) cc_final: 0.7958 (m110) REVERT: F 399 LYS cc_start: 0.7751 (mmmt) cc_final: 0.7366 (mttm) outliers start: 87 outliers final: 62 residues processed: 370 average time/residue: 0.1574 time to fit residues: 93.5871 Evaluate side-chains 373 residues out of total 2466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 303 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 266 HIS Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 387 GLN Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain C residue 295 MET Chi-restraints excluded: chain C residue 296 THR Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 380 ILE Chi-restraints excluded: chain C residue 387 GLN Chi-restraints excluded: chain C residue 425 ILE Chi-restraints excluded: chain C residue 430 LEU Chi-restraints excluded: chain C residue 449 VAL Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain D residue 207 MET Chi-restraints excluded: chain D residue 266 HIS Chi-restraints excluded: chain D residue 295 MET Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 370 SER Chi-restraints excluded: chain D residue 430 LEU Chi-restraints excluded: chain D residue 449 VAL Chi-restraints excluded: chain D residue 462 SER Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain D residue 490 THR Chi-restraints excluded: chain E residue 66 PHE Chi-restraints excluded: chain E residue 207 MET Chi-restraints excluded: chain E residue 215 ILE Chi-restraints excluded: chain E residue 262 GLN Chi-restraints excluded: chain E residue 306 VAL Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain E residue 387 GLN Chi-restraints excluded: chain E residue 430 LEU Chi-restraints excluded: chain E residue 449 VAL Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain E residue 490 THR Chi-restraints excluded: chain F residue 215 ILE Chi-restraints excluded: chain F residue 249 ILE Chi-restraints excluded: chain F residue 296 THR Chi-restraints excluded: chain F residue 306 VAL Chi-restraints excluded: chain F residue 312 VAL Chi-restraints excluded: chain F residue 418 LEU Chi-restraints excluded: chain F residue 425 ILE Chi-restraints excluded: chain F residue 430 LEU Chi-restraints excluded: chain F residue 449 VAL Chi-restraints excluded: chain F residue 450 SER Chi-restraints excluded: chain F residue 488 VAL Chi-restraints excluded: chain F residue 490 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 276 optimal weight: 0.9980 chunk 20 optimal weight: 8.9990 chunk 131 optimal weight: 0.0870 chunk 156 optimal weight: 0.9990 chunk 240 optimal weight: 0.9980 chunk 102 optimal weight: 6.9990 chunk 127 optimal weight: 9.9990 chunk 32 optimal weight: 0.0980 chunk 291 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 27 optimal weight: 9.9990 overall best weight: 0.6360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 HIS C 262 GLN C 431 ASN D 142 HIS F 262 GLN F 431 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.183242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.144604 restraints weight = 29489.299| |-----------------------------------------------------------------------------| r_work (start): 0.3715 rms_B_bonded: 1.98 r_work: 0.3517 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.3601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 23231 Z= 0.108 Angle : 0.510 10.555 31413 Z= 0.261 Chirality : 0.042 0.153 3432 Planarity : 0.004 0.032 4121 Dihedral : 4.025 18.601 3228 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 3.70 % Allowed : 15.54 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.49 (0.15), residues: 2952 helix: 2.29 (0.13), residues: 1596 sheet: 0.11 (0.26), residues: 378 loop : -0.88 (0.18), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 99 TYR 0.010 0.001 TYR B 528 PHE 0.034 0.001 PHE F 304 TRP 0.021 0.001 TRP E 338 HIS 0.003 0.001 HIS B 448 Details of bonding type rmsd covalent geometry : bond 0.00251 (23231) covalent geometry : angle 0.51004 (31413) hydrogen bonds : bond 0.03667 ( 1416) hydrogen bonds : angle 3.84243 ( 4050) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 2466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 336 time to evaluate : 0.865 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 PHE cc_start: 0.5723 (m-80) cc_final: 0.5235 (m-10) REVERT: A 281 GLU cc_start: 0.7745 (tp30) cc_final: 0.7445 (tp30) REVERT: A 282 ASN cc_start: 0.8140 (m-40) cc_final: 0.7737 (m110) REVERT: A 326 LYS cc_start: 0.8212 (mttp) cc_final: 0.7582 (ptmt) REVERT: A 338 TRP cc_start: 0.7348 (t-100) cc_final: 0.7001 (t-100) REVERT: A 370 SER cc_start: 0.6882 (OUTLIER) cc_final: 0.5994 (t) REVERT: A 373 GLU cc_start: 0.7077 (mp0) cc_final: 0.6675 (pm20) REVERT: A 399 LYS cc_start: 0.7668 (mmmt) cc_final: 0.7418 (mttm) REVERT: A 495 ASP cc_start: 0.7838 (m-30) cc_final: 0.7427 (m-30) REVERT: A 549 VAL cc_start: 0.8364 (t) cc_final: 0.8099 (t) REVERT: B 99 ARG cc_start: 0.7353 (mmm-85) cc_final: 0.6695 (mmm-85) REVERT: B 282 ASN cc_start: 0.8103 (m-40) cc_final: 0.7732 (m110) REVERT: B 326 LYS cc_start: 0.7954 (mtpt) cc_final: 0.7668 (mtpt) REVERT: B 349 GLU cc_start: 0.7327 (tm-30) cc_final: 0.7112 (mt-10) REVERT: B 387 GLN cc_start: 0.6975 (OUTLIER) cc_final: 0.6675 (mm110) REVERT: B 472 GLU cc_start: 0.8178 (mm-30) cc_final: 0.7811 (mm-30) REVERT: B 495 ASP cc_start: 0.7756 (m-30) cc_final: 0.7237 (m-30) REVERT: B 533 ASP cc_start: 0.8415 (t0) cc_final: 0.8146 (t0) REVERT: C 141 GLN cc_start: 0.7382 (OUTLIER) cc_final: 0.6911 (tp40) REVERT: C 281 GLU cc_start: 0.7765 (tp30) cc_final: 0.7456 (tp30) REVERT: C 282 ASN cc_start: 0.8266 (m-40) cc_final: 0.7928 (m110) REVERT: C 295 MET cc_start: 0.6968 (OUTLIER) cc_final: 0.6643 (ptt) REVERT: C 387 GLN cc_start: 0.7032 (OUTLIER) cc_final: 0.6755 (mp10) REVERT: C 399 LYS cc_start: 0.7772 (mmmt) cc_final: 0.7482 (mttm) REVERT: D 67 PHE cc_start: 0.5742 (m-80) cc_final: 0.5346 (m-10) REVERT: D 69 MET cc_start: 0.7079 (mtt) cc_final: 0.6800 (mtt) REVERT: D 281 GLU cc_start: 0.7707 (tp30) cc_final: 0.7403 (tp30) REVERT: D 282 ASN cc_start: 0.8082 (m-40) cc_final: 0.7790 (m110) REVERT: D 326 LYS cc_start: 0.8260 (mttp) cc_final: 0.7592 (ptmt) REVERT: D 338 TRP cc_start: 0.7451 (t-100) cc_final: 0.7158 (t-100) REVERT: D 399 LYS cc_start: 0.7699 (mmmt) cc_final: 0.7344 (mttm) REVERT: D 495 ASP cc_start: 0.7876 (m-30) cc_final: 0.7462 (m-30) REVERT: D 549 VAL cc_start: 0.8372 (t) cc_final: 0.8104 (t) REVERT: E 143 ARG cc_start: 0.8289 (mmm160) cc_final: 0.7009 (mpt-90) REVERT: E 262 GLN cc_start: 0.7898 (mm-40) cc_final: 0.7486 (mp10) REVERT: E 282 ASN cc_start: 0.8063 (m-40) cc_final: 0.7716 (m110) REVERT: E 326 LYS cc_start: 0.7644 (mtpt) cc_final: 0.7429 (mtpt) REVERT: E 387 GLN cc_start: 0.6822 (OUTLIER) cc_final: 0.6520 (mm110) REVERT: E 472 GLU cc_start: 0.8147 (mm-30) cc_final: 0.7782 (mm-30) REVERT: E 495 ASP cc_start: 0.7767 (m-30) cc_final: 0.7268 (m-30) REVERT: E 533 ASP cc_start: 0.8411 (t0) cc_final: 0.8115 (t0) REVERT: F 207 MET cc_start: 0.8331 (mtm) cc_final: 0.8063 (mtm) REVERT: F 281 GLU cc_start: 0.7788 (tp30) cc_final: 0.7450 (tp30) REVERT: F 282 ASN cc_start: 0.8208 (m-40) cc_final: 0.7852 (m110) REVERT: F 387 GLN cc_start: 0.7058 (OUTLIER) cc_final: 0.6836 (mm-40) REVERT: F 399 LYS cc_start: 0.7727 (mmmt) cc_final: 0.7433 (mttt) REVERT: F 533 ASP cc_start: 0.8524 (t0) cc_final: 0.7897 (t0) outliers start: 88 outliers final: 61 residues processed: 385 average time/residue: 0.1503 time to fit residues: 93.4922 Evaluate side-chains 384 residues out of total 2466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 316 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 380 ILE Chi-restraints excluded: chain B residue 387 GLN Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain C residue 141 GLN Chi-restraints excluded: chain C residue 262 GLN Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 295 MET Chi-restraints excluded: chain C residue 296 THR Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 387 GLN Chi-restraints excluded: chain C residue 425 ILE Chi-restraints excluded: chain C residue 430 LEU Chi-restraints excluded: chain C residue 449 VAL Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain D residue 207 MET Chi-restraints excluded: chain D residue 295 MET Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 425 ILE Chi-restraints excluded: chain D residue 430 LEU Chi-restraints excluded: chain D residue 462 SER Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain D residue 490 THR Chi-restraints excluded: chain E residue 306 VAL Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain E residue 387 GLN Chi-restraints excluded: chain E residue 401 ILE Chi-restraints excluded: chain E residue 425 ILE Chi-restraints excluded: chain E residue 430 LEU Chi-restraints excluded: chain E residue 449 VAL Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain E residue 490 THR Chi-restraints excluded: chain F residue 215 ILE Chi-restraints excluded: chain F residue 249 ILE Chi-restraints excluded: chain F residue 296 THR Chi-restraints excluded: chain F residue 306 VAL Chi-restraints excluded: chain F residue 312 VAL Chi-restraints excluded: chain F residue 380 ILE Chi-restraints excluded: chain F residue 387 GLN Chi-restraints excluded: chain F residue 425 ILE Chi-restraints excluded: chain F residue 430 LEU Chi-restraints excluded: chain F residue 449 VAL Chi-restraints excluded: chain F residue 450 SER Chi-restraints excluded: chain F residue 488 VAL Chi-restraints excluded: chain F residue 490 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 203 optimal weight: 5.9990 chunk 236 optimal weight: 2.9990 chunk 242 optimal weight: 3.9990 chunk 125 optimal weight: 0.0060 chunk 15 optimal weight: 4.9990 chunk 167 optimal weight: 8.9990 chunk 132 optimal weight: 4.9990 chunk 230 optimal weight: 0.8980 chunk 160 optimal weight: 0.9980 chunk 122 optimal weight: 9.9990 chunk 269 optimal weight: 0.9990 overall best weight: 1.1800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 GLN B 262 GLN E 262 GLN E 431 ASN F 262 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.180054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.140807 restraints weight = 29480.479| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 2.25 r_work: 0.3469 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.3865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 23231 Z= 0.137 Angle : 0.539 10.577 31413 Z= 0.277 Chirality : 0.044 0.154 3432 Planarity : 0.004 0.033 4121 Dihedral : 4.111 17.487 3228 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 4.07 % Allowed : 15.71 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.15), residues: 2952 helix: 2.34 (0.13), residues: 1560 sheet: 0.11 (0.27), residues: 366 loop : -0.94 (0.17), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 99 TYR 0.018 0.001 TYR D 528 PHE 0.033 0.002 PHE F 304 TRP 0.023 0.001 TRP E 338 HIS 0.003 0.001 HIS F 142 Details of bonding type rmsd covalent geometry : bond 0.00325 (23231) covalent geometry : angle 0.53868 (31413) hydrogen bonds : bond 0.04150 ( 1416) hydrogen bonds : angle 3.94341 ( 4050) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 2466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 311 time to evaluate : 0.917 Fit side-chains REVERT: A 67 PHE cc_start: 0.5772 (m-80) cc_final: 0.5531 (t80) REVERT: A 326 LYS cc_start: 0.8248 (mttp) cc_final: 0.7663 (ptmt) REVERT: A 370 SER cc_start: 0.6889 (OUTLIER) cc_final: 0.5926 (t) REVERT: A 399 LYS cc_start: 0.7666 (mmmt) cc_final: 0.7288 (mttm) REVERT: A 495 ASP cc_start: 0.7957 (m-30) cc_final: 0.7515 (m-30) REVERT: A 549 VAL cc_start: 0.8471 (t) cc_final: 0.8216 (t) REVERT: B 99 ARG cc_start: 0.7421 (mmm-85) cc_final: 0.6730 (mmm-85) REVERT: B 282 ASN cc_start: 0.8048 (m-40) cc_final: 0.7661 (m110) REVERT: B 319 TYR cc_start: 0.7835 (m-80) cc_final: 0.7480 (m-80) REVERT: B 387 GLN cc_start: 0.7066 (OUTLIER) cc_final: 0.6758 (mm110) REVERT: B 472 GLU cc_start: 0.8146 (mm-30) cc_final: 0.7775 (mm-30) REVERT: B 495 ASP cc_start: 0.7804 (m-30) cc_final: 0.7281 (m-30) REVERT: B 533 ASP cc_start: 0.8441 (t0) cc_final: 0.8157 (t0) REVERT: C 141 GLN cc_start: 0.7544 (OUTLIER) cc_final: 0.7042 (tp40) REVERT: C 282 ASN cc_start: 0.8309 (m-40) cc_final: 0.7988 (m110) REVERT: C 295 MET cc_start: 0.7104 (OUTLIER) cc_final: 0.6899 (ptt) REVERT: C 387 GLN cc_start: 0.7291 (OUTLIER) cc_final: 0.7017 (mm110) REVERT: C 399 LYS cc_start: 0.7811 (mmmt) cc_final: 0.7558 (mttt) REVERT: C 533 ASP cc_start: 0.8548 (t0) cc_final: 0.7939 (t0) REVERT: D 67 PHE cc_start: 0.5855 (m-80) cc_final: 0.5396 (m-10) REVERT: D 281 GLU cc_start: 0.7765 (tp30) cc_final: 0.7400 (tp30) REVERT: D 282 ASN cc_start: 0.8110 (m-40) cc_final: 0.7779 (m110) REVERT: D 311 ASN cc_start: 0.6996 (p0) cc_final: 0.6730 (m-40) REVERT: D 338 TRP cc_start: 0.7348 (t-100) cc_final: 0.7083 (t-100) REVERT: D 399 LYS cc_start: 0.7744 (mmmt) cc_final: 0.7379 (mttm) REVERT: D 495 ASP cc_start: 0.7983 (m-30) cc_final: 0.7536 (m-30) REVERT: D 549 VAL cc_start: 0.8439 (t) cc_final: 0.8196 (t) REVERT: E 99 ARG cc_start: 0.7493 (mmm-85) cc_final: 0.6715 (mmm-85) REVERT: E 282 ASN cc_start: 0.8121 (m-40) cc_final: 0.7732 (m110) REVERT: E 387 GLN cc_start: 0.7068 (OUTLIER) cc_final: 0.6772 (mm110) REVERT: E 495 ASP cc_start: 0.7832 (m-30) cc_final: 0.7335 (m-30) REVERT: E 533 ASP cc_start: 0.8408 (t0) cc_final: 0.8147 (t0) REVERT: F 207 MET cc_start: 0.8396 (mtm) cc_final: 0.8143 (mtm) REVERT: F 282 ASN cc_start: 0.8300 (m-40) cc_final: 0.7969 (m110) REVERT: F 349 GLU cc_start: 0.7425 (pp20) cc_final: 0.7203 (pp20) REVERT: F 399 LYS cc_start: 0.7846 (mmmt) cc_final: 0.7525 (mttt) REVERT: F 533 ASP cc_start: 0.8543 (t0) cc_final: 0.7942 (t0) outliers start: 97 outliers final: 63 residues processed: 371 average time/residue: 0.1544 time to fit residues: 91.9683 Evaluate side-chains 364 residues out of total 2466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 295 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain B residue 262 GLN Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 380 ILE Chi-restraints excluded: chain B residue 387 GLN Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain C residue 141 GLN Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 295 MET Chi-restraints excluded: chain C residue 296 THR Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 380 ILE Chi-restraints excluded: chain C residue 387 GLN Chi-restraints excluded: chain C residue 425 ILE Chi-restraints excluded: chain C residue 430 LEU Chi-restraints excluded: chain C residue 449 VAL Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain D residue 207 MET Chi-restraints excluded: chain D residue 295 MET Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 425 ILE Chi-restraints excluded: chain D residue 430 LEU Chi-restraints excluded: chain D residue 449 VAL Chi-restraints excluded: chain D residue 462 SER Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain D residue 490 THR Chi-restraints excluded: chain E residue 207 MET Chi-restraints excluded: chain E residue 262 GLN Chi-restraints excluded: chain E residue 306 VAL Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 387 GLN Chi-restraints excluded: chain E residue 401 ILE Chi-restraints excluded: chain E residue 430 LEU Chi-restraints excluded: chain E residue 449 VAL Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain E residue 490 THR Chi-restraints excluded: chain F residue 249 ILE Chi-restraints excluded: chain F residue 262 GLN Chi-restraints excluded: chain F residue 293 LEU Chi-restraints excluded: chain F residue 296 THR Chi-restraints excluded: chain F residue 306 VAL Chi-restraints excluded: chain F residue 312 VAL Chi-restraints excluded: chain F residue 380 ILE Chi-restraints excluded: chain F residue 425 ILE Chi-restraints excluded: chain F residue 430 LEU Chi-restraints excluded: chain F residue 449 VAL Chi-restraints excluded: chain F residue 450 SER Chi-restraints excluded: chain F residue 488 VAL Chi-restraints excluded: chain F residue 490 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 100 optimal weight: 6.9990 chunk 26 optimal weight: 8.9990 chunk 73 optimal weight: 1.9990 chunk 217 optimal weight: 3.9990 chunk 127 optimal weight: 9.9990 chunk 229 optimal weight: 7.9990 chunk 176 optimal weight: 6.9990 chunk 54 optimal weight: 3.9990 chunk 261 optimal weight: 0.7980 chunk 220 optimal weight: 0.9980 chunk 165 optimal weight: 0.9980 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 262 GLN C 262 GLN D 387 GLN ** D 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 262 GLN F 262 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.176627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.137199 restraints weight = 29361.635| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 2.22 r_work: 0.3419 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.4118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 23231 Z= 0.177 Angle : 0.583 10.325 31413 Z= 0.303 Chirality : 0.046 0.160 3432 Planarity : 0.004 0.034 4121 Dihedral : 4.295 17.708 3228 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 3.99 % Allowed : 15.46 % Favored : 80.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.15), residues: 2952 helix: 2.14 (0.13), residues: 1560 sheet: 0.01 (0.27), residues: 366 loop : -1.08 (0.17), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 136 TYR 0.016 0.002 TYR D 528 PHE 0.029 0.002 PHE F 304 TRP 0.024 0.001 TRP E 338 HIS 0.004 0.001 HIS F 142 Details of bonding type rmsd covalent geometry : bond 0.00423 (23231) covalent geometry : angle 0.58294 (31413) hydrogen bonds : bond 0.04572 ( 1416) hydrogen bonds : angle 4.06708 ( 4050) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 2466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 289 time to evaluate : 0.875 Fit side-chains REVERT: A 67 PHE cc_start: 0.5876 (m-80) cc_final: 0.5462 (m-10) REVERT: A 282 ASN cc_start: 0.8090 (m-40) cc_final: 0.7644 (m110) REVERT: A 326 LYS cc_start: 0.8305 (mttp) cc_final: 0.7687 (ptmt) REVERT: A 338 TRP cc_start: 0.7418 (t-100) cc_final: 0.7050 (t-100) REVERT: A 399 LYS cc_start: 0.7681 (mmmt) cc_final: 0.7275 (mttm) REVERT: A 495 ASP cc_start: 0.7997 (m-30) cc_final: 0.7554 (m-30) REVERT: B 141 GLN cc_start: 0.7419 (mp10) cc_final: 0.7104 (mp10) REVERT: B 282 ASN cc_start: 0.8081 (m-40) cc_final: 0.7676 (m110) REVERT: B 319 TYR cc_start: 0.7847 (m-80) cc_final: 0.7468 (m-80) REVERT: B 326 LYS cc_start: 0.7900 (mtpt) cc_final: 0.7138 (mtmt) REVERT: B 387 GLN cc_start: 0.7434 (OUTLIER) cc_final: 0.7050 (mm110) REVERT: B 495 ASP cc_start: 0.7836 (m-30) cc_final: 0.7325 (m-30) REVERT: B 533 ASP cc_start: 0.8434 (t0) cc_final: 0.8158 (t0) REVERT: C 282 ASN cc_start: 0.8302 (m-40) cc_final: 0.7945 (m110) REVERT: C 295 MET cc_start: 0.7257 (OUTLIER) cc_final: 0.7049 (ptt) REVERT: C 387 GLN cc_start: 0.7513 (OUTLIER) cc_final: 0.7206 (mm110) REVERT: C 399 LYS cc_start: 0.7887 (mmmt) cc_final: 0.7596 (mttt) REVERT: C 533 ASP cc_start: 0.8481 (t0) cc_final: 0.7972 (t0) REVERT: D 67 PHE cc_start: 0.5926 (m-80) cc_final: 0.5545 (m-10) REVERT: D 282 ASN cc_start: 0.8151 (m-40) cc_final: 0.7853 (m110) REVERT: D 311 ASN cc_start: 0.7055 (p0) cc_final: 0.6824 (m-40) REVERT: D 495 ASP cc_start: 0.8021 (m-30) cc_final: 0.7556 (m-30) REVERT: D 549 VAL cc_start: 0.8503 (t) cc_final: 0.8296 (t) REVERT: E 99 ARG cc_start: 0.7430 (mmm-85) cc_final: 0.6715 (mmm-85) REVERT: E 282 ASN cc_start: 0.8085 (m-40) cc_final: 0.7697 (m110) REVERT: E 387 GLN cc_start: 0.7487 (OUTLIER) cc_final: 0.7109 (mm110) REVERT: E 495 ASP cc_start: 0.7850 (m-30) cc_final: 0.7388 (m-30) REVERT: E 533 ASP cc_start: 0.8429 (t0) cc_final: 0.8157 (t0) REVERT: F 207 MET cc_start: 0.8383 (mtm) cc_final: 0.8141 (mtm) REVERT: F 399 LYS cc_start: 0.7932 (mmmt) cc_final: 0.7572 (mttt) REVERT: F 533 ASP cc_start: 0.8505 (t0) cc_final: 0.7979 (t0) outliers start: 95 outliers final: 74 residues processed: 347 average time/residue: 0.1582 time to fit residues: 87.5111 Evaluate side-chains 353 residues out of total 2466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 275 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain B residue 262 GLN Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 387 GLN Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 249 ILE Chi-restraints excluded: chain C residue 262 GLN Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 295 MET Chi-restraints excluded: chain C residue 296 THR Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 380 ILE Chi-restraints excluded: chain C residue 387 GLN Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 425 ILE Chi-restraints excluded: chain C residue 430 LEU Chi-restraints excluded: chain C residue 449 VAL Chi-restraints excluded: chain C residue 450 SER Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain D residue 207 MET Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 295 MET Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 430 LEU Chi-restraints excluded: chain D residue 449 VAL Chi-restraints excluded: chain D residue 462 SER Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain D residue 490 THR Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 207 MET Chi-restraints excluded: chain E residue 262 GLN Chi-restraints excluded: chain E residue 306 VAL Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 387 GLN Chi-restraints excluded: chain E residue 401 ILE Chi-restraints excluded: chain E residue 418 LEU Chi-restraints excluded: chain E residue 430 LEU Chi-restraints excluded: chain E residue 449 VAL Chi-restraints excluded: chain E residue 462 SER Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain E residue 490 THR Chi-restraints excluded: chain F residue 249 ILE Chi-restraints excluded: chain F residue 262 GLN Chi-restraints excluded: chain F residue 293 LEU Chi-restraints excluded: chain F residue 296 THR Chi-restraints excluded: chain F residue 306 VAL Chi-restraints excluded: chain F residue 312 VAL Chi-restraints excluded: chain F residue 380 ILE Chi-restraints excluded: chain F residue 418 LEU Chi-restraints excluded: chain F residue 425 ILE Chi-restraints excluded: chain F residue 430 LEU Chi-restraints excluded: chain F residue 449 VAL Chi-restraints excluded: chain F residue 450 SER Chi-restraints excluded: chain F residue 488 VAL Chi-restraints excluded: chain F residue 490 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 57 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 chunk 0 optimal weight: 9.9990 chunk 27 optimal weight: 0.2980 chunk 7 optimal weight: 4.9990 chunk 262 optimal weight: 4.9990 chunk 240 optimal weight: 3.9990 chunk 166 optimal weight: 0.5980 chunk 249 optimal weight: 1.9990 chunk 272 optimal weight: 7.9990 chunk 67 optimal weight: 3.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 262 GLN C 262 GLN E 262 GLN F 262 GLN ** F 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.177857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.138997 restraints weight = 29457.250| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 1.97 r_work: 0.3436 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3281 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.4207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 23231 Z= 0.151 Angle : 0.569 10.966 31413 Z= 0.294 Chirality : 0.045 0.174 3432 Planarity : 0.004 0.036 4121 Dihedral : 4.230 17.333 3228 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 3.57 % Allowed : 15.41 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.15), residues: 2952 helix: 2.14 (0.13), residues: 1560 sheet: -0.17 (0.26), residues: 378 loop : -0.99 (0.17), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 99 TYR 0.012 0.001 TYR D 528 PHE 0.027 0.002 PHE F 304 TRP 0.026 0.001 TRP E 338 HIS 0.004 0.001 HIS F 142 Details of bonding type rmsd covalent geometry : bond 0.00360 (23231) covalent geometry : angle 0.56946 (31413) hydrogen bonds : bond 0.04292 ( 1416) hydrogen bonds : angle 4.04340 ( 4050) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 2466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 290 time to evaluate : 0.903 Fit side-chains REVERT: A 67 PHE cc_start: 0.6061 (m-80) cc_final: 0.5640 (m-10) REVERT: A 282 ASN cc_start: 0.8191 (m-40) cc_final: 0.7719 (m110) REVERT: A 326 LYS cc_start: 0.8357 (mttp) cc_final: 0.7702 (ptmt) REVERT: A 399 LYS cc_start: 0.7748 (mmmt) cc_final: 0.7298 (mttm) REVERT: A 495 ASP cc_start: 0.8210 (m-30) cc_final: 0.7775 (m-30) REVERT: B 262 GLN cc_start: 0.8287 (OUTLIER) cc_final: 0.8073 (mp10) REVERT: B 282 ASN cc_start: 0.8183 (m-40) cc_final: 0.7787 (m110) REVERT: B 319 TYR cc_start: 0.7856 (m-80) cc_final: 0.7500 (m-80) REVERT: B 326 LYS cc_start: 0.7911 (mtpt) cc_final: 0.7163 (mtmt) REVERT: B 349 GLU cc_start: 0.7429 (pp20) cc_final: 0.6762 (pt0) REVERT: B 387 GLN cc_start: 0.7525 (OUTLIER) cc_final: 0.7191 (mm110) REVERT: B 495 ASP cc_start: 0.8047 (m-30) cc_final: 0.7538 (m-30) REVERT: B 533 ASP cc_start: 0.8558 (t0) cc_final: 0.8267 (t0) REVERT: C 387 GLN cc_start: 0.7549 (OUTLIER) cc_final: 0.7213 (mm110) REVERT: C 399 LYS cc_start: 0.7975 (mmmt) cc_final: 0.7578 (mttt) REVERT: C 533 ASP cc_start: 0.8607 (t0) cc_final: 0.8046 (t0) REVERT: D 67 PHE cc_start: 0.5953 (m-80) cc_final: 0.5501 (m-10) REVERT: D 282 ASN cc_start: 0.8230 (m-40) cc_final: 0.7882 (m110) REVERT: D 311 ASN cc_start: 0.7138 (p0) cc_final: 0.6856 (m-40) REVERT: D 338 TRP cc_start: 0.7671 (t-100) cc_final: 0.7282 (t-100) REVERT: D 399 LYS cc_start: 0.7882 (mmmt) cc_final: 0.7382 (mttt) REVERT: D 495 ASP cc_start: 0.8270 (m-30) cc_final: 0.7820 (m-30) REVERT: E 282 ASN cc_start: 0.8218 (m-40) cc_final: 0.7850 (m110) REVERT: E 326 LYS cc_start: 0.7976 (mtpt) cc_final: 0.7376 (mtmt) REVERT: E 387 GLN cc_start: 0.7510 (OUTLIER) cc_final: 0.7191 (mm110) REVERT: E 485 ILE cc_start: 0.8374 (OUTLIER) cc_final: 0.8148 (tp) REVERT: E 495 ASP cc_start: 0.8028 (m-30) cc_final: 0.7558 (m-30) REVERT: E 533 ASP cc_start: 0.8548 (t0) cc_final: 0.8261 (t0) REVERT: F 207 MET cc_start: 0.8661 (mtm) cc_final: 0.8408 (mtm) REVERT: F 282 ASN cc_start: 0.8799 (t0) cc_final: 0.8471 (t0) REVERT: F 317 MET cc_start: 0.7393 (ptp) cc_final: 0.7184 (ptp) REVERT: F 373 GLU cc_start: 0.7126 (mp0) cc_final: 0.6745 (mp0) REVERT: F 399 LYS cc_start: 0.7990 (mmmt) cc_final: 0.7560 (mttt) REVERT: F 412 GLU cc_start: 0.7824 (pm20) cc_final: 0.7385 (tm-30) REVERT: F 533 ASP cc_start: 0.8658 (t0) cc_final: 0.8082 (t0) outliers start: 85 outliers final: 71 residues processed: 336 average time/residue: 0.1522 time to fit residues: 82.7046 Evaluate side-chains 346 residues out of total 2466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 270 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain B residue 262 GLN Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 387 GLN Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 249 ILE Chi-restraints excluded: chain C residue 262 GLN Chi-restraints excluded: chain C residue 296 THR Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 380 ILE Chi-restraints excluded: chain C residue 387 GLN Chi-restraints excluded: chain C residue 425 ILE Chi-restraints excluded: chain C residue 430 LEU Chi-restraints excluded: chain C residue 449 VAL Chi-restraints excluded: chain C residue 450 SER Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain D residue 207 MET Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 295 MET Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 380 ILE Chi-restraints excluded: chain D residue 425 ILE Chi-restraints excluded: chain D residue 430 LEU Chi-restraints excluded: chain D residue 449 VAL Chi-restraints excluded: chain D residue 462 SER Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain D residue 490 THR Chi-restraints excluded: chain E residue 207 MET Chi-restraints excluded: chain E residue 262 GLN Chi-restraints excluded: chain E residue 306 VAL Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 387 GLN Chi-restraints excluded: chain E residue 401 ILE Chi-restraints excluded: chain E residue 418 LEU Chi-restraints excluded: chain E residue 425 ILE Chi-restraints excluded: chain E residue 430 LEU Chi-restraints excluded: chain E residue 449 VAL Chi-restraints excluded: chain E residue 485 ILE Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain E residue 490 THR Chi-restraints excluded: chain F residue 215 ILE Chi-restraints excluded: chain F residue 249 ILE Chi-restraints excluded: chain F residue 262 GLN Chi-restraints excluded: chain F residue 293 LEU Chi-restraints excluded: chain F residue 296 THR Chi-restraints excluded: chain F residue 306 VAL Chi-restraints excluded: chain F residue 312 VAL Chi-restraints excluded: chain F residue 380 ILE Chi-restraints excluded: chain F residue 418 LEU Chi-restraints excluded: chain F residue 425 ILE Chi-restraints excluded: chain F residue 430 LEU Chi-restraints excluded: chain F residue 449 VAL Chi-restraints excluded: chain F residue 450 SER Chi-restraints excluded: chain F residue 488 VAL Chi-restraints excluded: chain F residue 490 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 77 optimal weight: 4.9990 chunk 206 optimal weight: 0.7980 chunk 141 optimal weight: 3.9990 chunk 142 optimal weight: 1.9990 chunk 147 optimal weight: 9.9990 chunk 37 optimal weight: 2.9990 chunk 254 optimal weight: 1.9990 chunk 166 optimal weight: 4.9990 chunk 50 optimal weight: 0.8980 chunk 160 optimal weight: 0.7980 chunk 49 optimal weight: 6.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.177239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.138747 restraints weight = 29556.257| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 1.91 r_work: 0.3439 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3284 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.4278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 23231 Z= 0.148 Angle : 0.570 9.897 31413 Z= 0.296 Chirality : 0.045 0.192 3432 Planarity : 0.004 0.037 4121 Dihedral : 4.236 17.584 3228 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 3.11 % Allowed : 15.67 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.15), residues: 2952 helix: 2.22 (0.13), residues: 1524 sheet: -0.11 (0.27), residues: 366 loop : -0.94 (0.17), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 99 TYR 0.012 0.001 TYR A 170 PHE 0.028 0.002 PHE F 304 TRP 0.026 0.001 TRP E 338 HIS 0.004 0.001 HIS F 142 Details of bonding type rmsd covalent geometry : bond 0.00351 (23231) covalent geometry : angle 0.57008 (31413) hydrogen bonds : bond 0.04263 ( 1416) hydrogen bonds : angle 4.04582 ( 4050) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 2466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 272 time to evaluate : 0.901 Fit side-chains revert: symmetry clash REVERT: A 67 PHE cc_start: 0.6034 (m-80) cc_final: 0.5628 (m-10) REVERT: A 282 ASN cc_start: 0.8135 (m-40) cc_final: 0.7644 (m110) REVERT: A 326 LYS cc_start: 0.8337 (mttp) cc_final: 0.7702 (ptmt) REVERT: A 399 LYS cc_start: 0.7727 (mmmt) cc_final: 0.7403 (mttm) REVERT: A 495 ASP cc_start: 0.8291 (m-30) cc_final: 0.7844 (m-30) REVERT: B 282 ASN cc_start: 0.8191 (m-40) cc_final: 0.7804 (m110) REVERT: B 319 TYR cc_start: 0.7893 (m-80) cc_final: 0.7533 (m-80) REVERT: B 326 LYS cc_start: 0.7858 (mtpt) cc_final: 0.7163 (mtmt) REVERT: B 349 GLU cc_start: 0.7378 (pp20) cc_final: 0.6724 (pt0) REVERT: B 387 GLN cc_start: 0.7530 (OUTLIER) cc_final: 0.7266 (mm110) REVERT: B 495 ASP cc_start: 0.8043 (m-30) cc_final: 0.7539 (m-30) REVERT: B 533 ASP cc_start: 0.8573 (t0) cc_final: 0.8312 (t0) REVERT: C 326 LYS cc_start: 0.8181 (tttt) cc_final: 0.7650 (mtmt) REVERT: C 387 GLN cc_start: 0.7536 (OUTLIER) cc_final: 0.7218 (mm110) REVERT: C 399 LYS cc_start: 0.7965 (mmmt) cc_final: 0.7653 (mttt) REVERT: C 533 ASP cc_start: 0.8608 (t0) cc_final: 0.8048 (t0) REVERT: D 67 PHE cc_start: 0.5900 (m-80) cc_final: 0.5539 (m-10) REVERT: D 282 ASN cc_start: 0.8173 (m-40) cc_final: 0.7787 (m110) REVERT: D 311 ASN cc_start: 0.7138 (p0) cc_final: 0.6897 (m-40) REVERT: D 338 TRP cc_start: 0.7636 (t-100) cc_final: 0.7294 (t-100) REVERT: D 399 LYS cc_start: 0.7809 (mmmt) cc_final: 0.7322 (mttt) REVERT: D 495 ASP cc_start: 0.8269 (m-30) cc_final: 0.7825 (m-30) REVERT: E 282 ASN cc_start: 0.8197 (m-40) cc_final: 0.7832 (m110) REVERT: E 326 LYS cc_start: 0.7966 (mtpt) cc_final: 0.7481 (mttt) REVERT: E 387 GLN cc_start: 0.7550 (OUTLIER) cc_final: 0.7228 (mm110) REVERT: E 485 ILE cc_start: 0.8384 (OUTLIER) cc_final: 0.8146 (tp) REVERT: E 495 ASP cc_start: 0.8029 (m-30) cc_final: 0.7563 (m-30) REVERT: E 533 ASP cc_start: 0.8486 (t0) cc_final: 0.8229 (t0) REVERT: F 207 MET cc_start: 0.8661 (mtm) cc_final: 0.8417 (mtm) REVERT: F 282 ASN cc_start: 0.8735 (t0) cc_final: 0.8410 (t0) REVERT: F 349 GLU cc_start: 0.7555 (pp20) cc_final: 0.6890 (pt0) REVERT: F 373 GLU cc_start: 0.7101 (mp0) cc_final: 0.6712 (mp0) REVERT: F 399 LYS cc_start: 0.8025 (mmmt) cc_final: 0.7562 (mttt) REVERT: F 412 GLU cc_start: 0.7834 (pm20) cc_final: 0.7348 (tm-30) REVERT: F 533 ASP cc_start: 0.8620 (t0) cc_final: 0.8064 (t0) outliers start: 74 outliers final: 69 residues processed: 312 average time/residue: 0.1535 time to fit residues: 78.1674 Evaluate side-chains 339 residues out of total 2466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 266 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 387 GLN Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 249 ILE Chi-restraints excluded: chain C residue 296 THR Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 380 ILE Chi-restraints excluded: chain C residue 387 GLN Chi-restraints excluded: chain C residue 425 ILE Chi-restraints excluded: chain C residue 430 LEU Chi-restraints excluded: chain C residue 449 VAL Chi-restraints excluded: chain C residue 450 SER Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain D residue 207 MET Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 306 VAL Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 380 ILE Chi-restraints excluded: chain D residue 425 ILE Chi-restraints excluded: chain D residue 430 LEU Chi-restraints excluded: chain D residue 449 VAL Chi-restraints excluded: chain D residue 462 SER Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain D residue 490 THR Chi-restraints excluded: chain E residue 207 MET Chi-restraints excluded: chain E residue 306 VAL Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 387 GLN Chi-restraints excluded: chain E residue 401 ILE Chi-restraints excluded: chain E residue 418 LEU Chi-restraints excluded: chain E residue 425 ILE Chi-restraints excluded: chain E residue 430 LEU Chi-restraints excluded: chain E residue 449 VAL Chi-restraints excluded: chain E residue 485 ILE Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain E residue 490 THR Chi-restraints excluded: chain F residue 215 ILE Chi-restraints excluded: chain F residue 249 ILE Chi-restraints excluded: chain F residue 293 LEU Chi-restraints excluded: chain F residue 296 THR Chi-restraints excluded: chain F residue 306 VAL Chi-restraints excluded: chain F residue 312 VAL Chi-restraints excluded: chain F residue 380 ILE Chi-restraints excluded: chain F residue 401 ILE Chi-restraints excluded: chain F residue 418 LEU Chi-restraints excluded: chain F residue 425 ILE Chi-restraints excluded: chain F residue 430 LEU Chi-restraints excluded: chain F residue 449 VAL Chi-restraints excluded: chain F residue 450 SER Chi-restraints excluded: chain F residue 488 VAL Chi-restraints excluded: chain F residue 490 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 35 optimal weight: 4.9990 chunk 280 optimal weight: 0.9990 chunk 179 optimal weight: 4.9990 chunk 164 optimal weight: 5.9990 chunk 20 optimal weight: 8.9990 chunk 108 optimal weight: 0.6980 chunk 104 optimal weight: 0.7980 chunk 15 optimal weight: 0.6980 chunk 271 optimal weight: 7.9990 chunk 157 optimal weight: 1.9990 chunk 227 optimal weight: 2.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 262 GLN C 262 GLN C 282 ASN E 262 GLN F 262 GLN F 282 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.178822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.139504 restraints weight = 29376.606| |-----------------------------------------------------------------------------| r_work (start): 0.3656 rms_B_bonded: 2.16 r_work: 0.3459 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.4332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 23231 Z= 0.132 Angle : 0.556 13.167 31413 Z= 0.287 Chirality : 0.044 0.156 3432 Planarity : 0.004 0.037 4121 Dihedral : 4.145 17.157 3228 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 3.32 % Allowed : 15.83 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.33 (0.15), residues: 2952 helix: 2.30 (0.13), residues: 1524 sheet: -0.25 (0.26), residues: 378 loop : -0.83 (0.18), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 99 TYR 0.011 0.001 TYR D 528 PHE 0.027 0.002 PHE F 304 TRP 0.026 0.001 TRP E 338 HIS 0.003 0.001 HIS F 142 Details of bonding type rmsd covalent geometry : bond 0.00310 (23231) covalent geometry : angle 0.55580 (31413) hydrogen bonds : bond 0.04014 ( 1416) hydrogen bonds : angle 3.99380 ( 4050) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5692.64 seconds wall clock time: 98 minutes 39.07 seconds (5919.07 seconds total)